Amido and peptido modified enzymatic nucleic acid molecules

ABSTRACT

Oligonucleotide comprising a nucleotide base having the formula: ##STR1## wherein B is a nucleotide base or hydrogen; R 1 , R 2  and R 3  independently is selected from the group consisting of hydrogen, an alkyl group containing between 2 and 10 carbon atoms inclusive, an amine, an amino acid, and a peptide containing between 2 and 5 amino acids inclusive; and the zigzag lines are independently hydrogen or a bond.

RELATED APPLICATIONS

This application is a continuation of application Ser. No. 08/357,577,filed Dec. 16, 1994, now U.S. Pat. No. 5,783,425, which is acontinuation-in-part of application Ser. No. 08/143,832, filed Oct. 27,1993, now abandoned, the whole of which, including drawings, are herebyincorporated by reference herein.

BACKGROUND OF THE INVENTION

This invention relates to modifications of oligonucleotides.

Usman et al., "Nucleozymes", International Application No. PCT/US93/00833, describes modification of the 2'-hydroxyl -group of RNA toproduce modified nucleotides. Such nucleotides are termed nucleic acidanalogs, and may have a "good coordinating ligand" with divalent metalions, e.g., a halogen, or amine group. Acyclic analogs are alsodescribed.

Eckstein, International Application No. PCT/EP91/01811 (WO 92/07065),describes 2'-hydroxyl modifications of RNA having the followingsubstitutions in place of the hydroxyl group: halo, sulfhydryl, azido,amino, mono-substituted amino and di-substituted amino.

Sproat et al., 1994 "Synthetic catalytic oligonucleotide structures",U.S. Pat. No. 5,334,711, describes hammerhead ribozymes which containnucleotides having 2'-OR modifications where, O represents oxygen and Rrepresents H, or alkyl, alkenyl, or alkinyl.

Buhr and Matteucci, International Application No. WO 91/06556, describes2'-hydroxyl modifications of antisense oligonucleotides with NHAcmodifications.

SUMMARY OF THE INVENTION

This invention relates to replacement of the 2'-hydroxyl group of aribonucleotide moiety with a 2'-amido or 2'-peptido moiety. In otherembodiments, the 3' and 5' portions of the sugar of a nucleotide may besubstituted, or the phosphate group may be substituted with amido orpeptido moieties. Generally, such a nucleotide has the general structureshown in Formula I below: ##STR2##

FORMULA I

The base (B) is any one of the standard bases or is a modifiednucleotide base known to those in the art, or can be a hydrogen group.In addition, either R₁ or R₂ is H or an alkyl, alkene or alkyne groupcontaining between 2 and 10 carbon atoms, or hydrogen, an amine(primary, secondary or tertiary, e.g., R₃ NR₄ where each R₃ and R₄independently is hydrogen or an alkyl, alkene or alkyne having between 2and 10 carbon atoms, or is a residue of an amino acid, i.e., an amide),an alkyl group, or an amino acid (D or L forms) or peptide containingbetween 2 and 5 amino acids. The zigzag lines represent hydrogen, or abond to another base or other chemical moiety known in the art.Preferably, one of R₁, R₂ and R₃ is an H, and the other is an amino acidor peptide.

Applicant has recognized that RNA can assume a much more complexstructural form than DNA because of the presence of the 2'-hydroxylgroup in RNA. This group is able to provide additional hydrogen bondingwith other hydrogen donors, acceptors and metal ions within the RNAmolecule. Applicant now provides molecules which have a modified aminegroup at the 2' position, such that significantly more complexstructures can be formed by the modified oligonucleotide. Suchmodification with a 2'-amido or peptido group leads to expansion andenrichment of the side-chain hydrogen bonding network. The amide andpeptide moieties are responsible for complex structural formation of theoligonucleotide and can form strong complexes with other bases, andinterfere with standard base pairing interactions. Such interferencewill allow the formation of a complex nucleic acid and proteinconglomerate.

Oligonucleotides of this invention are significantly more stable thanexisting oligonucleotides and can potentially form biologically activebioconjugates not previously possible for oligonucleotides. They mayalso be used for in vitro selection of unique aptamers, that is,randomly generated oligonucleotides which can be folded into aneffective ligand for a target protein, nucleic acid or polysaccharide.

Thus, in a first aspect, the invention features an oligonucleotidecontaining the modified base shown in Formula I, above.

In other aspects, the oligonucleotide may include a 3' or 5' nucleotidehaving a 3' or 5' located amino acid or aminoacyl group. In all theseaspects, as well as the 2'-modified nucleotide, it will be evident thatvarious standard modifications can be made. For example, an "O" may bereplaced with an S, the sugar may lack a base (i.e., abasic) and thephosphate moiety may be modified to include other substitutions (seeSproat, supra).

Other features and advantages of the invention will be apparent from thefollowing description of the preferred embodiments thereof, and from theclaims.

DESCRIPTION OF THE PREFERRED EMBODIMENTS

The drawings will first briefly be described.

Drawings

FIG. 1 is a diagrammatic representation of the hammerhead ribozymedomain known in the art. Stem II can be ≧2 base-pair long.

FIGS. 2a-d: FIG. 2a is a diagrammatic representation of the hammerheadribozyme domain known in the art; FIG. 2b is a diagrammaticrepresentation of the hammerhead ribozyme as divided by Uhlenbeck (1987,Nature, 327, 596-600) into a substrate and enzyme portion; FIG. 2c is asimilar diagram showing the hammerhead divided by Haseloff and Gerlach(1988, Nature, 334, 585-591) into two portions; and FIG. 2d is a similardiagram showing the hammerhead divided by Jeffries and Symons (1989,Nucl. Acids. Res., 17, 1371-1371) into two portions.

FIG. 3 is a diagrammatic representation of the general structure of ahairpin ribozyme. Helix 2 (H2) is provided with a least 4 base pairs(i.e., n is 1, 2, 3 or 4) and helix 5 can be optionally provided oflength 2 or more bases (preferably 3-20 bases, i.e., m is from 1-20 ormore). Helix 2 and helix 5 may be covalently linked by one or more bases(i.e., r is ≧1 base). Helix 1, 4 or 5 may also be extended by 2 or morebase pairs (e.g., 4-20 base pairs) to stabilize the ribozyme structure,and preferably is a protein binding site. In each instance, each N andN' independently is any normal or modified base and each dash representsa potential base-pairing interaction. These nucleotides may be modifiedat the sugar, base or phosphate. Complete base-pairing is not requiredin the helices, but is preferred. Helix 1 and 4 can be of any size(i.e., o and p is each independently from 0 to any number, e.g., 20) aslong as some base-pairing is maintained. Essential bases are shown asspecific bases in the structure, but those in the art will recognizethat one or more may be modified chemically (abasic, base, sugar and/orphosphate modifications) or replaced with another base withoutsignificant effect. Helix 4 can be formed from two separate molecules,i.e., without a connecting loop. The connecting loop when present may bea ribonucleotide with or without modifications to its base, sugar orphosphate. "q" is ≧2 bases. The connecting loop can also be replacedwith a non-nucleotide linker molecule. H , refers to bases A, U or C. Yrefers to pyrimidine bases."

FIG. 4 is a representation of the general structure of the hepatitisdelta virus ribozyme domain known in the art.

FIG. 5 is a representation of the general structure of the self-cleavingVS RNA ribozyme domain.

FIG. 6 is a schematic representation of synthesizing RNA phosphoramiditeof a nucleotide containing a 2'-hydroxyl group modification of thepresent invention.

FIG. 7 describes a method for deprotection of oligonucleotidescontaining a 2'-hydroxyl group modification of the present invention.

FIG. 8 is a diagrammatic representation of a hammerhead ribozymetargeted to site A. Positions of 2'-hydroxyl group substitution isindicated.

FIG. 9 shows RNA cleavage activity of ribozymes containing a 2'-hydroxylgroup modification of the present invention. All RNA, representshammerhead ribozyme (HHA) with no 2'-hydroxyl group modifications.U7-ala, represents HHA ribozyme containing 2'-NH-alanine modification atthe U7 position. U4/U7-ala, represents HHA containing 2'-NH-alaninemodifications at U4 and U7 positions. U4 lys, represents HHA containing2'-NH-lysine modification at U4 position. U7 lys, represents HHAcontaining 2'-NH-lysine modification at U7 position. U4/U7-lys,represents HHA containing 2'-NH-lysine modification at U4 and U7positions.

FIGS. 10A and B: FIG. 10A is a schematic representation of synthesizing(solid-phase synthesis) 3' ends of RNA with modification of the presentinvention. FIG. 10B, refers to either a base, modified base or an H.

FIGS. 11A and B FIG. 11A is a schematic representation of synthesizing(solid-phase synthesis) 5' ends of RNA with modification of the presentinvention. FIG. 11B, refers to either a base, modified base or an H.

Oligonucleotides of this invention are described generally above, andthe structure is shown in Formula I, where such modifications to the2'-hydroxyl group can be made in one or more positions of an RNA or DNAmolecule. Preferably, the oligonucleotide is single-stranded and hasbetween 10 and 50 bases of which one or more may be modified as shown,preferably, between 1 and 10 are modified. Such oligonucleotides mayinclude those having enzymatic activity, i.e., ribozymes, which aremodified in the 2'- position of the sugar moiety as shown in Formula Ito provide stability to that enzymatic activity without significantalteration of the activity.

Oligonucleotides of the present invention can be readily synthesizedusing carbamate protecting groups, such as F-moc, in the peptidemoieties and deprotected under mild basic conditions. Such nucleotidescan then be incorporated by standard solid-phase synthesis usingnucleoside phosphoramidite or H-phosphonate intermediates.

Uses

The above nucleotides are particularly useful in ribozymes. Ribozymesare RNA molecules having an enzymatic activity which is able torepeatedly cleave other separate RNA molecules in a nucleotide basesequence specific manner. Such enzymatic RNA molecules can be targetedto virtually any RNA transcript, and efficient cleavage achieved invitro. Kim et al., 84 Proc. Natl. Acad. Sci. USA 8788, 1987; Haseloffand Gerlach, 334 Nature 585, 1988; Cech, 260 JAMA 3030, 1988; andJefferies et al., 17 Nucleic Acids Research 1371, 1989.

Ribozymes act by first binding to a target RNA. Such binding occursthrough the target RNA binding portion of a ribozyme which is held inclose proximity to an enzymatic portion of the RNA which acts to cleavethe target RNA. Thus, the ribozyme first recognizes and then binds atarget RNA through complementary base-pairing, and once bound to thecorrect site, acts enzymatically to cut the target RNA. Strategiccleavage of such a target RNA will destroy its ability to directsynthesis of an encoded protein. After a ribozyme has bound and cleavedits RNA target it is released from that RNA to search for another targetand can repeatedly bind and cleave new targets.

By "complementarity" is meant a nucleic acid that can form hydrogenbond(s) with other RNA sequence by either traditional Watson-Crick orother non-traditional types (for example, Hoogsteen type) of base-pairedinteractions.

Six basic varieties of naturally-occurring enzymatic RNAs are knownpresently. Each can catalyze the hydrolysis of RNA phosphodiester bondsin trans (and thus can cleave other RNA molecules) under physiologicalconditions. Table I summarizes some of the characteristics of theseribozymes. In general, enzymatic nucleic acids act by first binding to atarget RNA. Such binding occurs through the target binding portion of aenzymatic nucleic acid which is held in close proximity to an enzymaticportion of the molecule that acts to cleave the target RNA. Thus, theenzymatic nucleic acid first recognizes and then binds a target RNAthrough complementary base-pairing, and once bound to the correct site,acts enzymatically to cut the target RNA. Strategic cleavage of such atarget RNA will destroy its ability to direct synthesis of an encodedprotein. After an enzymatic nucleic acid has bound and cleaved its RNAtarget, it is released from that RNA to search for another target andcan repeatedly bind and cleave new targets.

The enzymatic nature of a ribozyme is advantageous over othertechnologies, such as antisense technology (where a nucleic acidmolecule simply binds to a nucleic acid target to block its translation)since the effective concentration of ribozyme necessary to effect atherapeutic treatment is lower than that of an antisenseoligonucleotide. This advantage reflects the ability of the ribozyme toact enzymatically. Thus, a single ribozyme molecule is able to cleavemany molecules of target RNA. In addition, the ribozyme is a highlyspecific inhibitor, with the specificity of inhibition depending notonly on the base pairing mechanism of binding, but also on the mechanismby which the molecule inhibits the expression of the RNA to which itbinds. That is, the inhibition is caused by cleavage of the RNA targetand so specificity is defined as the ratio of the rate of cleavage ofthe targeted RNA over the rate of cleavage of non-targeted RNA. Thiscleavage mechanism is dependent upon factors additional to thoseinvolved in base pairing. Thus, it is thought that the specificity ofaction of a ribozyme is greater than that of antisense oligonucleotidebinding the same RNA site.

By "enzymatic RNA molecule" it is meant an RNA molecule which hascomplementarity in a substrate binding region to a specified genetarget, and also has an enzymatic activity which is active tospecifically cleave RNA in that target. That is, the enzymatic RNAmolecule is able to intermolecularly cleave RNA and thereby inactivate atarget RNA molecule. This complementarity functions to allow sufficienthybridization of the enzymatic RNA molecule to the target RNA to allowthe cleavage to occur. One hundred percent complementarity is preferred,but complementarity as low as 50-75% may also be useful in thisinvention.

In preferred embodiments of this invention, the enzymatic nucleic acidmolecule is formed in a hammerhead or hairpin motif, but may also beformed in the motif of a hepatitis delta virus, group I intron or RNasePRNA (in association with an RNA guide sequence) or Neurospora VS RNA.Examples of such hammerhead motifs are described by Rossi et al., 1992,Aids Research and Human Retroviruses 8, 183, of hairpin motifs by Hampelet al., EP0360257, Hampel and Tritz, 1989 Biochemistry 28, 4929, andHampel et al., 1990 Nucleic Acids Res. 18, 299, and an example of thehepatitis delta virus motif is described by Perrotta and Been, 1992Biochemistry 31, 16; of the RNaseP motif by Guerrier-Takada et al., 1983Cell 35, 849, Neurospora VS RNA ribozyme motif is described by Collins(Saville and Collins, 1990 Cell 61, 685-696; Saville and Collins, 1991Proc. Natl. Acad. Sci. USA 88, 8826-8830; Collins and Olive, 1993Biochemistry 32, 2795-2799) and of the Group I intron by Cech et al.,U.S. Pat. No. 4,987,071. These specific motifs are not limiting in theinvention and those skilled in the art will recognize that all that isimportant in an enzymatic nucleic acid molecule of this invention isthat it has a specific substrate binding site which is complementary toone or more of the target gene RNA regions, and that it have nucleotidesequences within or surrounding that substrate binding site which impartan RNA cleaving activity to the molecule.

In a preferred embodiment the invention provides a method for producinga class of enzymatic cleaving agents which exhibit a high degree ofspecificity for the RNA of a desired target. The enzymatic nucleic acidmolecule is preferably targeted to a highly conserved sequence region ofa target RNAs such that specific treatment of a disease or condition canbe provided with either one or several enzymatic nucleic acids. Suchenzymatic nucleic acid molecules can be delivered exogenously tospecific cells as required.

Synthesis of Ribozymes

Synthesis of nucleic acids greater than 100 nucleotides in length isdifficult using automated methods, and the therapeutic cost of suchmolecules is prohibitive. In this invention, small enzymatic nucleicacid motifs (e.g., of the hammerhead or the hairpin structure), are usedfor exogenous delivery. The simple structure of these moleculesincreases the ability of the enzymatic nucleic acid to invade targetedregions of the mRNA structure.

The ribozymes are chemically synthesized. The method of synthesis usedfollows the procedure for normal RNA synthesis as described in Usman etal., 1987 J. Am. Chem. Soc., 109, 7845 and in Scaringe et al., 1990Nucleic Acids Res., 18, 5433 and makes use of common nucleic acidprotecting and coupling groups, such as dimethoxytrityl at the 5'-end,and phosphoramidites at the 3'-end. The average stepwise coupling yieldswere >98%.

Ribozymes are purified by gel electrophoresis using general methods orare purified by high pressure liquid chromatography (HPLC; See Usman etal., Synthesis, deprotection, analysis and purification of RNA andribozymes, filed May, 18, 1994, U.S. Ser. No. 08/245,736 the totality ofwhich is hereby incorporated herein by reference) and are resuspended inwater.

Various modifications to ribozyme structure can be made to enhance theutility of ribozymes. Such modifications will enhance shelf-life,half-life in vitro, stability, and ease of introduction of suchribozymes to the target site, e.g., to enhance penetration of cellularmembranes, and confer the ability to recognize and bind to targetedcells.

Optimizing Ribozyme Activity

Ribozyme activity can be optimized as described by Stinchcomb et al.,"Method and Composition for Treatment of Restenosis and Cancer UsingRibozymes," filed May 18, 1994, U.S. Ser. No. 08/245,466. The detailswill not be repeated here, but include altering the length of theribozyme binding arms (stems I and III, see FIG. 2c), or chemicallysynthesizing ribozymes with modifications that prevent their degradationby serum ribonucleases (see e.g., Eckstein et al., InternationalPublication No. WO 92/07065; Perrault et al., 1990 Nature 344, 565;Pieken et al., 1991 Science 253, 314; Usman and Cedergren, 1992 Trendsin Biochem. Sci. 17, 334; Usman et al., International Publication No. WO93/15187; and Rossi et al., International Publication No. WO 91/03162,as well as Usman, N. et al. U.S. patent application Ser. No. 07/829,729,and Sproat, European Patent Application 92110298.4 which describevarious chemical modifications that can be made to the sugar moieties ofenzymatic RNA molecules. Modifications which enhance their efficacy incells, and removal of stem II bases to shorten RNA synthesis times andreduce chemical requirements. (All these publications are herebyincorporated by reference herein.).

Administration of Ribozyme

Sullivan et al., PCT WO 094/02595, describes the general methods fordelivery of enzymatic RNA molecules. Ribozymes may be administered tocells by a variety of methods known to those familiar to the art,including, but not restricted to, encapsulation in liposomes, byiontophoresis, or by incorporation into other vehicles, such ashydrogels, cyclodextrins, biodegradable nanocapsules, and bioadhesivemicrospheres. For some indications, ribozymes may be directly deliveredex vivo to cells or tissues with or without the aforementioned vehicles.Alternatively, the RNA/vehicle combination is locally delivered bydirect injection or by use of a catheter, infusion pump or stent. Otherroutes of delivery include, but are not limited to, intravascular,intramuscular, subcutaneous or joint injection, aerosol inhalation, oral(tablet or pill form), topical, systemic, ocular, intraperitoneal and/orintrathecal delivery. More detailed descriptions of ribozyme deliveryand administration are provided in Sullivan et al., supra and Draper etal., PCT WO93/23569 which have been incorporated by reference herein.

EXAMPLE 1

General procedure for the preparation of2'-aminoacyl-2'-deoxy-2'-aminonucleoside conjugates

Referring to FIG. 6, to the solution of 2'-deoxy-2'-amino nucleoside (1mmol) and N-Fmoc L- (or D-) amino acid (1 mmol) in methanol[dimethylformamide (DMF) and tetrahydrofuran (THF) can also be used],1-ethoxycarbonyl-2-ethoxy-1,2-dihydroquinoline (EEDQ) [or1-isobutyloxycarbonyl-2-isobutyloxy-1,2-dihydroquinoline (IIDQ)] (2mmol) is added and the reaction mixture is stirred at room temperatureor up to 50° C. from 3-48 hours. Solvents are removed under reducedpressure and the residual syrup is chromatographed on the column ofsilica-gel using 1-10% methanol in dichloromethane. Fractions containingthe product are concentrated yielding a white foam with yields rangingfrom 85 to 95%. Structures are confirmed by ¹ H NMR spectra ofconjugates which show correct chemical shifts for nucleoside andaminoacyl part of the molecule. Further proofs of the structures areobtained by cleaving the aminoacyl protecting groups under appropriateconditions and assigning ¹ H NMR resonances for the fully deprotectedconjugate.

Partially protected conjugates described above are converted into their5'-O-dimethoxytrityl derivatives and into 3'-phosphoramidites usingstandard procedures (Oligonucleotide Synthesis: A Practical Approach, M.J. Gait ed.; IRL Press, Oxford, 1984). Incorporation of thesephosphoramidites into RNA was performed using standard protocols (Usmanet al., 1987 supra).

A general deprotection protocol for oligonucleotides of the presentinvention is described in FIG. 7.

The scheme shows synthesis of conjugate of 2'-d-2'-aminouridine. This ismeant to be a non-limiting example, and those skilled in the art willrecognize that, variations to the synthesis protocol can be readilygenerated to synthesize other nucelotides (e.g., adenosine, cytidine,guanosine) and/or abasic moieties.

EXAMPLE 2

RNA cleavage by hammerhead ribozymes containing 2'-aminoacylmodifications

Hammerhead ribozymes targeted to site A (see FIG. 8) are synthesizedusing solid-phase synthesis, as described above. U4 and U7 positions aremodified, individually or in combination, with either 2'-NH-alanine or2'-NH-lysine.

RNA cleavage assay in vitro: Substrate RNA is 5' end-labeled using [γ-³²P] ATP and T4 polynucleotide kinase (US Biochemicals). Cleavagereactions were carried out under ribozyme "excess" conditions. Traceamount (≦1 nM) of 5' end-labeled substrate and 40 nM unlabeled ribozymeare denatured and renatured separately by heating to 90° C. for 2 minand snap-cooling on ice for 10 -15 min. The ribozyme and substrate areincubated, separately, at 37° C. for 10 min in a buffer containing 50 mMTris-HCl and 10 mM MgCl₂. The reaction is initiated by mixing theribozyme and substrate solutions and incubating at 37° C. Aliquots of 5μl are taken at regular intervals of time and the reaction is quenchedby mixing with equal volume of 2X formamide stop mix. The samples areresolved on 20% denaturing polyacrylamide gels. The results arequantified and percentage of target RNA cleaved is plotted as a functionof time.

Referring to FIG. 9, hammerhead ribozymes containing 2'-NH-alanine or2'-NH-lysine modifications at U4 and U7 positions cleave the target RNAefficiently.

Sequences listed in FIG. 8 and the modifications described in FIG. 9 aremeant to be non-limiting examples. Those skilled in the art willrecognize that variants (base-substitutions, deletions, insertions,mutations, chemical modifications) of the ribozyme and RNA containingother 2'-hydroxyl group modifications, including but not limited toamino acids, peptides and cholesterol, can be readily generated usingtechniques known in the art, and are within the scope of the presentinvention.

EXAMPLE 3

Aminoacylation of 3'-ends of RNA

I. Referring to FIG. 10A, 3'-OH group of the nucleotide is converted tosuccinate as described by Gait, supra. This can be linked withamino-alkyl solid support (for example: CpG). Zig-zag line indicateslinkage of 3'OH group with the solid support.

II. Preparation of aminoacyl-derivatized solid support

A) Synthesis of O-Dimethoxytrityl (O-DMT) amino acids

Referring to FIG. 10B, to a solution of L- (or D-) serine, tyrosine orthreonine (2 mmol) in dry pyridine (15 ml) 4,4'-dimethoxytrityl chloride(3 mmol) is added and the reaction mixture is stirred at RT (about20-25° C.) for 16 h. Methanol (10 ml) is then added and the solutionevaporated under reduced pressure. The residual syrup was partitionedbetween 5% aq. NaHCO₃ and dichloromethane, organic layer was washed withbrine, dried (Na₂ SO₄) and concentrated in vacuo. The residue ispurified by flash silicagel column chromatography using 2-10% methanolin dichloromethane (containing 0.5% pyridine). Fractions containingproduct are combined and concentrated in vacuo to yield white foam(75-85% yield).

B) Preparation of the solid support and its derivatization with aminoacids

Referring to FIG. 10B, the modified solid support (has an OH groupinstead of the standard NH₂ end group) was prepared according toHaralambidis et al., Tetrahedron Lett. 1987, 28, 5199, (P denotesaminopropyl CPG or polystyrene type support). O-DMT orNH-monomethoxytrityl (NH-MMT amino acid was attached to the above solidsupport using standard procedures for derivatization of the solidsupport (Gait, 1984, supra) creating a base-labile ester bond betweenamino acids and the support. This support is suitable for theconstruction of RNA/DNA chain using suitably protected nucleosidephosphoramidites.

EXAMPLE 4

Aminoacylation of 5'-ends of RNA

I. Referring to FIG. 11A, 5'-amino-containing sugar moiety wassynthesized as described (Mag and Engels, 1989 Nucleic Acids Res. 17,5973). Aminoacylation of the 5'-end of the monomer was achieved asdescribed above and RNA phosphoramidite of the 5'-aminoacylated monomerwas prepared as described by Usman et al., 1987 supra. Thephosphoramidite was then incorporated at the 5'-end of theoligonucleotide using standard solid-phase synthesis protocols describedabove.

II. Referring to FIG. 11 B, aminoacyl group(s) is attached to thephosphate group at the 5'-end of the RNA using standard proceduresdescribed above.

Diagnostic Uses

Ribozymes of this invention may be used as diagnostic tools to examinegenetic drift and mutations within diseased cells or to detect thepresence of target RNA in a cell. The close relationship betweenribozyme activity and the structure of the target RNA allows thedetection of mutations in any region of the molecule which alters thebase-pairing and three-dimensional structure of the target RNA. By usingmultiple ribozymes described in this invention, one may map nucleotidechanges which are important to RNA structure and function in vitro, aswell as in cells and tissues. Cleavage of target RNAs with ribozymes maybe used to inhibit gene expression and define the role (essentially) ofspecified gene products in the progression of disease. In this manner,other genetic targets may be defined as important mediators of thedisease. These experiments will lead to better treatment of the diseaseprogression by affording the possibility of combinational therapies(e.g., multiple ribozymes targeted to different genes, ribozymes coupledwith known small molecule inhibitors, or intermittent treatment withcombinations of ribozymes and/or other chemical or biologicalmolecules). Other in vitro uses of ribozymes of this invention are wellknown in the art, and include detection of the presence of mRNAsassociated with target related condition. Such RNA is detected bydetermining the presence of a cleavage product after treatment with aribozyme using standard methodology.

In a specific example, ribozymes which can cleave only wild-type ormutant forms of the target RNA are used for the assay. The firstribozyme is used to identify wild-type RNA present in the sample and thesecond ribozyme will be used to identify mutant RNA in the sample. Asreaction controls, synthetic substrates of both wild-type and mutant RNAwill be cleaved by both ribozymes to demonstrate the relative ribozymeefficiencies in the reactions and the absence of cleavage of the"non-targeted" RNA species. The cleavage products from the syntheticsubstrates will also serve to generate size markers for the analysis ofwild-type and mutant RNAs in the sample population. Thus each analysiswill require two ribozymes, two substrates and one unknown sample whichwill be combined into six reactions. The presence of cleavage productswill be determined using an RNAse protection assay so that full-lengthand cleavage fragments of each RNA can be analyzed in one lane of apolyacrylamide gel. It is not absolutely required to quantify theresults to gain insight into the expression of mutant RNAs and putativerisk of the desired phenotypic changes in target cells. The expressionof mRNA whose protein product is implicated in the development of thephenotype is adequate to establish risk. If probes of comparablespecific activity are used for both transcripts, then a qualitativecomparison of RNA levels will be adequate and will decrease the cost ofthe initial diagnosis. Higher mutant form to wild-type ratios will becorrelated with higher risk whether RNA levels are comparedqualitatively or quantitatively.

Other embodiments are within the following claims.

                  TABLE I                                                         ______________________________________                                        Characteristics of Ribozymes                                                  ______________________________________                                        Group 1 Introns                                                                Size: ˜200 to >1000 nucleotides.                                        Requires a U in the target sequence immediately 5' of the cleavage            site.                                                                         Binds 4-6 nucleotides at 5' side of cleavage site.                            Over 75 known members of this class. Found in Tetrahymena                     thermophila rRNA, fungal mitochondria, chloroplasts, phage T4, blue-          green algae, and others.                                                      RNAseP RNA (M1 RNA)                                                           Size: -290 to 400 nucleotides.                                                RNA portion of a ribonucleoprotein enzyme. Cleaves tRNA precursors            to form mature tRNA.                                                          Roughly 10 known members of this group all are bacterial in origin.           Hammerhead Ribozyme                                                           Size: ˜13 to 40 nucleotides.                                            Requires the target sequence UH immediately 5' of the cleavage site.          Binds a variable number nucleotides on both side of the cleavage              site.                                                                         14 known members of this class. Found in a number of plant                    pathogens (virusoids) that use RNA as the infectious agent (FIGS. 1           and 2)                                                                        Hairpin Ribozyme                                                              Size: ˜50 nucleotides.                                                  Requires the target sequence GUC immediately 3' of the cleavage site.         Binds 4-6 nucleotides at 5' side of the cleavage site and a variable          number to the 3' side of the cleavage site.                                   Only 3 known member of this class. Found in three plant pathogen              (satellite RNAs of the tobacco ringspot virus, arabis mosaic virus            and chicory yellow mottle virus) which uses RNA as the                        infectious agent (FIG. 3).                                                    Hepatitis Delta Virus (HDV) Ribozyme                                          Size: 50-60 nucleotides (at present).                                         Cleavage of target RNAs recently demonstrated.                                Sequence requirements not fully determined.                                   Binding sites and structural requirements not fully determined,               although no sequences 5' of cleavage site are required.                       Only 1 known member of this class. Found in human HDV (FIG. 4).               Neurospora VS RNA Ribozyme                                                    Size: ˜144 nucleotides (at present)                                     Cleavage of target RNAs recently demonstrated.                                Sequence requirements not fully determined.                                   Binding sites and structural requirements not fully determined. Only 1        known member of this class. Found in Neurospara VS RNA (FIG. 5).             ______________________________________                                    

We claim:
 1. An enzymatic nucleic acid molecule with endonucleaseactivity to cleave a separate RNA molecule, wherein said enzymaticnucleic acid molecule comprises a substrate binding site which iscomplementary to the separate RNA molecule and a nucleotide sequencewithin or surrounding said substrate binding site wherein saidnucleotide sequence imparts to said enzymatic nucleic acid moleculeactivity for the cleavage of the separate RNA molecule, wherein saidenzymatic nucleic acid molecule further comprises a moiety having theformula I: ##STR3## wherein B is a nucleotide base or hydrogen; R isselected from the group consisting of an aminoacyl group, and a NHR₄group, wherein said R₄ is independently selected from the groupconsisting of a peptidyl group containing between 2 and 5 amino acidsinclusive, and CO-CR₁ R₂ R₃, wherein R₁, R₂ and R₃ are independentlyselected from the group consisting of hydrogen, and an alkyl groupcontaining between 2 and 10 carbon atoms inclusive.
 2. The enzymaticnucleic acid molecule of claim 1, wherein said enzymatic nucleic acidmolecule is chemically synthesized.
 3. The enzymatic nucleic acidmolecule of claim 1, wherein said enzymatic nucleic acid molecule is ina purified form.
 4. The enzymatic nucleic acid molecule of claim 1,wherein said enzymatic nucleic acid molecule is active in the presenceof divalent metal ions.
 5. The enzymatic nucleic acid molecule of claim1, wherein said enzymatic nucleic acid molecule is in a hammerheadmotif.
 6. A method of cleaving a separate RNA molecule, comprising thestep of contacting said separate RNA molecule with the enzymatic nucleicacid molecule of claim 1 under conditions suitable for the cleavage ofsaid separate RNA molecule.
 7. A method of inactivating a target RNAmolecule, comprising the step of cleaving said target RNA with anenzymatic nucleic acid molecule of claim 1 under conditions suitable forsaid inactivation of the target RNA.
 8. A mammalian cell in culturecomprising an enzymatic nucleic acid molecule of claim
 1. 9. Themammalian cell of claim 8, wherein said mammalian cell is a human cell.10. The mammalian cell of claim 8, wherein said enzymatic nucleic acidmolecule is active in the presence of divalent metal ions.
 11. Themammalian cell of claim 8, wherein said enzymatic nucleic acid moleculeis in a hammerhead motif.